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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgcacccagcttaatcatctgtatgtgcagagaacacctttattttcatactgaacgttgcttcacttaatacttcattacctataatctgtggcagGTGGAACGATCTAGCAGTTCTTACAGCCAGCACAGGCCTAGAAGGCCTCCCCCTGACTTGCCATCATTGCTTCTTCATGGCCGAATTGTTTACATTGGCA

Basic information

species Oryza sativa
transcript LOC_Os03g22430.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G030072_T01 (Zea mays), 3'ss of exon 1
taatgcacccagcttaatcatctgtatgtgcagagaacacctttatt-ttcatact------gaacgttgcttcacttaatacttcattacctataatctgtgg----cagGTGGAACGATCTAGCAGTTCTTACAGCCAGCACAGGCCTAGAAGGCCTCCCCCTGACTTGCCATCATTGCTTCTTCATGGCCGAATTGTTTACATTGGCA
              | |||  |||||||  |   ||  | ||||  | ||  || |      ||||    ||||||||||   | |||| ||| |  | |||      ||||||||||| |||||||| || || || |||||||| |||||||||||||| || || ||||| |||||||||||||| |||||||| ||||| |||||||
-----------ctgttatctgctgtatgcaccttgatgatctttggtatttgtagtatatacgaactgcacttcacttaaccatacattgcctctgctttgtaattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCTCCAGATTTGCCTTCATTGCTTCTTCACGGCCGAATCGTTTATATTGGCA

upper sequence: LOC_Os03g22430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA03G39570.1 (Glycine max), 3'ss of exon 1
taatgcacccagcttaatcatctgtatgtgcagagaacacctttattttca-tactgaacgttgcttcacttaatacttcattacctataat--ctgtggcagGTGGAACGATCTAGCAGTTCTTACAGCCAGCACAGGCCTAGAAGGCCTCCCCCTGACTTGCCATCATTGCTTCTTCATGGCCGAATTGTTTACATTGGCA---
   | |     |  | ||    ||||||  |   | | |  | ||||| |  || | |   ||   ||      ||  ||| | | |    |   ||    |||| ||| |||||     ||| |||| | | ||| | || |||||||| || |||||| |||| ||  ||||||| |||||  ||||||||||||||||||   
--ttcctaagtgtgttatagagtgtatgctctttgta-atttgtatttcctctagtcatgcttatctcttgaggtaactcaatccattgtgtggttgaattagGTTGAAAGATCT---GTTTCATACAACGAACACCGACCCAGAAGGCCACCGCCTGACCTGCCTTCGCTGCTTCTCCATGGTAGAATTGTTTACATTGGCATGC

upper sequence: LOC_Os03g22430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA19G42180.2 (Glycine max), 3'ss of exon 1
taatgcacccagcttaatcatctgtat-gtgcagagaac-----acctttattttc-atactgaacgttgcttcacttaatacttca-ttacctata-atctgtggcagGTGGAACGATCTAGCAGTTCTTACAGCCAGCACAGGCCTAGAAGGCCTCCCCCTGACTTGCCATCATTGCTTCTTCATGGCCGAATTGTTTACATTGGCA---
           ||| | | | || ||| ||| | |  |      |  | ||||| |  || | |   ||   |       ||  ||| |||  | |     ||    |||| ||| | |||     ||| |||| | | ||| |||| |||||||| || |||||| |||| ||  ||||||| |||||  ||||||||||||||||||   
---------tggctgagtgacctatatagtgtatactatttgtaatttgtatttcctgtagtcatgcttatatgttggggtaactcaattaattgtgtggttgaattagGTTGAAAGGTCT---GTTTCATACAACGAACACCGGCCCAGAAGGCCGCCACCTGACCTGCCTTCGCTGCTTCTCCATGGTAGAATTGTTTACATTGGCATGC

upper sequence: LOC_Os03g22430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0060g02160.t01 (Vitis vinifera), 3'ss of exon 1
taatgcacccagcttaatc-atctgtatgtgcagagaacacctttattttcatactgaacgttgcttcacttaatactt-cattacctataatctgtggcagGTGGAACGATCTAGCAGTTCTTACAGCCAGCACAGGCCTAGAAGGCCTCCCCCTGACTTGCCATCATTGCTTCTTCATGGCCGAATTGTTTACATTGGCA---
 | ||     |   |||   || |    ||      |||    | |  | | || |   | || |||   |   || ||   || ||| |  | |     |||||||| |||||  |   || ||||   |||||||||| || |||||||| || |||||||| ||  ||||||| |||||  |||| |||||||||||||   
-agtgtctttaaaataaaggatataagagtttctgtaac-taatcagctacttaatattcatttcttggttatctatttgtttttcctttggtttaaattagGTGGAAAGATCTGTC---TCGTACAATGAGCACAGGCCAAGGAGGCCTCCACCGGACTTGCCTTCCCTGCTTCTCCATGGGAGAATAGTTTACATTGGCATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcatactgaacgttgcttcacttaatacttcattacctataatctgtggcagGTGGAACGATCTAGCAGTTCTTACAGCCAGCACAGGCCTAGAAGGCCTCCCCCTGACTTGCCATCATTGCTTCTTCATGGCCGAATTGTTTACATTGGCA
                      acttaat  putative branch site (score: 4)
                        ttaatacttcatta  TA-rich tract